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Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation

Item Type:Article
Title:Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation
Creators Name:Graf, R. and Munschauer, M. and Mastrobuoni, G. and Mayr, F. and Heinemann, U. and Kempa, S. and Rajewsky, N. and Landthaler, M.
Abstract:The conserved human LIN28 RNA-binding proteins function in development, maintenance of pluripotency and oncogenesis. We used PAR-CLIP and a newly developed variant of this method, iDo-PAR-CLIP, to identify LIN28B targets as well as sites bound by the individual RNA-binding domains of LIN28B in the human transcriptome at nucleotide resolution. The position of target binding sites reflected the known structural relative orientation of individual LIN28B-binding domains, validating iDo-PAR-CLIP. Our data suggest that LIN28B directly interacts with most expressed mRNAs and members of the let-7 microRNA family. The Lin28-binding motif detected in pre-let-7 was enriched in mRNA sequences bound by LIN28B. Upon LIN28B knockdown, cell proliferation and the cell cycle were strongly impaired. Quantitative shotgun proteomics of LIN28B depleted cells revealed significant reduction of protein synthesis from its RNA targets that function in translation, mRNA splicing and cell cycle control. Computational analyses provided evidence that the strength of protein synthesis reduction correlated with the location of LIN28B binding sites within target transcripts.
Keywords:CLIP, RNA-Binding Protein, Post-Transcriptional Regulation, Stem Cell
Source:RNA Biology
ISSN:1547-6286
Publisher:Landes Bioscience (U.S.A)
Volume:10
Number:7
Page Range:1146-1159
Date:1 July 2013
Official Publication:https://doi.org/10.4161/rna.25194
PubMed:View item in PubMed

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